The foreign and defence ministers of Japan and Russia have agreed to increase co-operation between their military forces, in their first high level defence talks in years.

Japan's foreign minister Fumio Kishida and defence minister Itsunori Onodera held a meeting with Russia's foreign minister Sergei Lavrov and defence minister Sergei Shoigu on Saturday at the government's guest house in Tokyo.

It was the first such diplomatic-defence talks between the two countries, which remain at odds over the sovereignty of a cluster of islands to Japan's north and Russia's far east.

During the one-day meeting, the two sides agreed to carry out joint drills between Japan's Maritime Self-Defence Force and the Russian Navy designed to combat terrorists and pirates, the ministers said.

They also agreed to launch "Japan-Russia cyber-security talks" while stepping up other security and defence talks, including ministerial meetings, according to their joint statement.

"We got off to a good start by turning to a new chapter of the Japanese and Russian relationship," Japanese foreign minister Fumio Kishida said.

"Pushing for cooperation in the security sector will help enhance the entire relationship between Japan and Russia, which will have a good impact on negotiations on signing a peace treaty," he said.